Background
Methods
Patient datasets
Variables | TCGA cohort (n = 301) | Discovery cohort (n = 150) | Validation cohort (n = 151) | P-value | |
---|---|---|---|---|---|
Stage, no(%) | I | 207 (68.8) | 106 (70.7) | 101 (66.9) | 0.726a |
II | 16 (5.3) | 9 (6) | 7 (4.6) | ||
III | 64 (21.3) | 30 (20) | 34 (22.5) | ||
IV | 13 (4.3) | 5 (3.3) | 8 (5.3) | ||
Grade, no(%) | 1 | 70 (23.3) | 33 (22) | 37 (24.5) | 0.619a |
2 | 81 (26.9) | 38 (25.3) | 43 (28.5) | ||
3 | 150 (49.8) | 79 (52.7) | 71 (47) | ||
histology, no(%) | Endometrioid | 243 (80.7) | 124 (82.7) | 119 (78.8) | 0.664a |
Serous | 50 (16.6) | 22 (14.7) | 28 (18.5) | ||
Mixed | 8 (2.7) | 4 (2.7) | 4 (2.6) | ||
Vital status, no(%) | Alive | 270 (89.7) | 133 (88.7) | 137 (90.7) | 0.69a |
Dead | 31 (10.3) | 17 (11.3) | 14 (9.3) | ||
Age, years (mean ± SD) | 63.4 ± 10.7 | 63.7 ± 11.1 | 63.0 ± 10.4 | 0.537b |
Acquisition and processing of mRNA and lncRNA expression profiles in UCEC patients
Statistical analysis
Formulation of lncRNA-focus expression signature
In silico analysis of lncRNA function
Result
Patient’s characteristics
Development of lncRNA-focus expression signature for survival prediction in UCEC
Ensembl id | Gene symbol | Genomic location | Coefficient | Hazard ratio | 95% CI | P Value |
---|---|---|---|---|---|---|
ENSG00000260684 | RP11-1072A3.3.1 | chr16: 30,995,950–30,999,591 | 2.695 | 14.805 | 3.546–61.82 | <0.001 |
ENSG00000229589 | ACVR2B-AS1 | chr 3: 38,451,027–38,454,820 | 1.038 | 2.823 | 1.522–5.237 | 0.001 |
ENSG00000224037 | RP4-781 K5.7.1 | chr1: 234,845,004–234,855,723 | 2.331 | 10.289 | 2.419–43.76 | 0.002 |
ENSG00000235499 | AC073046.25 | chr 2: 73,985,132–73,986,343 | 0.798 | 2.220 | 1.337–3.687 | 0.002 |
ENSG00000224905 | AP001347.6 | chr 21: 14,027,421–14,144,468 | 0.722 | 2.058 | 1.297–3.264 | 0.002 |
ENSG00000260992 | DOCK9-AS2 | chr 13: 99,087,819–99,088,625 | 0.306 | 1.358 | 1.11–1.661 | 0.003 |
ENSG00000248008 | NRAV | chr 12: 120,490,328–120,495,940 | −0.236 | 0.790 | 0.67–0.9313 | 0.005 |
ENSG00000234945 | GTF3C2-AS1 | chr 2: 27,335,535–27,342,599 | 4.013 | 55.321 | 3.258–939.3 | 0.005 |
ENSG00000182648 | LINC01006 | chr 7: 156,472,196–156,640,654 | 0.665 | 1.945 | 1.208–3.133 | 0.006 |
ENSG00000253636 | RP11-531A24.5 | chr 8: 73,052,178–73,063,061 | 0.410 | 1.507 | 1.107–2.052 | 0.009 |
ENSG00000233760 | AC004947.2 | chr 7: 26,551,822–26,557,200 | 0.172 | 1.187 | 1.042–1.353 | 0.010 |
Prognostic validation of LFES in the discovery cohort
Variables | Unfavorable/Favorable | Univariate | Multivariate | ||||
---|---|---|---|---|---|---|---|
HR | 95% CI | P vaule | HR | 95% CI | P vaule | ||
Discovery cohort (n = 150) | |||||||
11-lncRNA risk score | High/Low | 2.718 | 1.923–3.842 | <0.001 | 2.649 | 1.788–3.923 | <0.001 |
Age | 1.055 | 1.004–1.108 | 0.035 | 0.992 | 0.931–1.057 | 0.797 | |
Stage | (III + IV)/(I + II) | 4.122 | 1.588–10.7 | 0.004 | 1.219 | 0.392–3.795 | 0.732 |
Grade | 3/(1 + 2) | 4.397 | 1.258–15.37 | 0.020 | 1.609 | 0.397–6.52 | 0.506 |
Histology | Serous/Endometrioid | 1.731 | 0.604–4.962 | 0.307 | 0.728 | 0.217–2.445 | 0.607 |
Validation cohort (n = 151) | |||||||
11-lncRNA risk score | High/Low | 6.903 | 1.521–31.340 | 0.012 | 6.158 | 1.205–31.465 | 0.029 |
Age | 1.042 | 0.986–1.101 | 0.141 | 1.046 | 0.975–1.122 | 0.208 | |
Stage | (III + IV)/(I + II) | 7.160 | 2.196–23.340 | 0.001 | 7.153 | 1.601–31.955 | 0.010 |
Grade | 3/(1 + 2) | 2.632 | 0.879–7.885 | 0.084 | 0.681 | 0.150–3.083 | 0.618 |
Histology | Serous/Endometrioid | 4.873 | 1.627–14.600 | 0.005 | 0.691 | 0.099–4.830 | 0.709 |
Entire TCGA cohort (n = 301) | |||||||
11-lncRNA risk score | High/Low | 11.767 | 3.568–38.810 | <0.001 | 10.793 | 3.084–37.777 | <0.001 |
Age | 1.050 | 1.012–1.09 | 0.009 | 1.064 | 1.018–1.112 | 0.006 | |
Stage | (III + IV)/(I + II) | 4.835 | 2.359–9.906 | <0.001 | 3.948 | 1.759–8.859 | 0.001 |
Grade | 3/(1 + 2) | 3.206 | 1.433–7.177 | 0.005 | 1.263 | 0.490–3.257 | 0.628 |
Histology | Serous/Endometrioid | 2.584 | 1.236–5.402 | 0.012 | 0.509 | 0.209–1.240 | 0.137 |